Flow Diagram
Matthew Hoctor, Bryon Langford
7/4/2021
Preliminary Flow Chart
#Set the values which will go into each label.
a1 <- 'Total available patients\n(n = x)'
b1 <- ''
c1 <- ''
d1 <- 'Included for analysis\n(n = x - y - z)'
e1 <- 'Data linked with\nexternal dataset'
a2 <- ''
b2 <- 'Excluded because of\nexclusion criteria (n = y)'
c2 <- 'Excluded because of\nmissing values (n = z)'
d2 <- ''
e2 <- ''
#Create a node dataframe
ndf <- create_node_df(
n = 10,
label = c(a1, b1, c1, d1, e1, #Column 1
a2, b2, c2, d2, e2), #Column 2
style = c('solid', 'invis', 'invis', 'solid', 'solid', #Column 1
'invis', 'solid', 'solid', 'invis', 'invis'), #Column 2
shape = c('box', 'point', 'point', 'box', 'box', #Column 1
'plaintext', 'box', 'box', 'point', 'point'), #Column 2
width = c(3, 0.001, 0.001, 3, 3, #Column 1
2, 2.5, 2.5, 0.001, 0.001), #Column 2
height = c(1, 0.001, 0.001, 1, 1, #Column 1
1, 1, 1, 0.001, 0.001), #Column 2
fontsize = c(rep(14, 10)),
fontname = c(rep('Helvetica', 10)),
penwidth = 1.5,
fixedsize = 'true')
#Create an edge dataframe
edf <- create_edge_df(
from = c(1, 2, 3, 4, #Column 1
6, 7, 8, 9, #Column 2
2, 3 #Horizontals
),
to = c(2, 3, 4, 5, #Column 1
7, 8, 9, 10, #Column 2
7, 8 #Horizontals
),
arrowhead = c('none', 'none', 'normal', 'normal', #Column 1
'none', 'none', 'none', 'none', #Column 2
'normal', 'normal' #Horizontals
),
color = c('black', 'black', 'black', 'black', #Column 1
'#00000000', '#00000000', '#00000000', '#00000000', #Column 2
'black', 'black' #Horizontals
),
constraint = c(rep('true', 8), #Columns
rep('false', 2) #Horizontals
)
)
g <- create_graph(ndf,
edf,
attr_theme = NULL)
#Not run: but to run this in R Studio, uncomment below
render_graph(g)#export_graph(g, file_name = "STROBE.png")Preliminary Flow Chart 2
# Define some sample data
data <- list(a=50000, b=800, c=600, d=400)
DiagrammeR::grViz("
digraph graph2 {
graph [layout = dot]
# node definitions with substituted label text
node [shape = rectangle, width = 4, fillcolor = Biege]
a [label = '@@1']
b [label = '@@2']
c [label = '@@3']
d [label = '@@4']
e [label = '@@5']
a -> b -> c -> d
a -> e
}
[1]: paste0('NHANES Data 2007-2018 (n = ', data$a, ')')
[2]: paste0('Remove Errors (n = ', data$b, ')')
[3]: paste0('Identify Potential Customers (n = ', data$c, ')')
[4]: paste0('Select Top Priorities (n = ', data$d, ')')
[5]: paste0('Select Top Priorities (n = ', data$d, ')')
")Gmisc method flowchart
Documentation https://cran.r-project.org/web/packages/Gmisc/vignettes/Grid-based_flowcharts.html
org_cohort <- boxGrob(glue("Stockholm population",
"n = {pop}",
pop = txtInt(1632798),
.sep = "\n"))
eligible <- boxGrob(glue("Eligible",
"n = {pop}",
pop = txtInt(10032),
.sep = "\n"))
included <- boxGrob(glue("Randomized",
"n = {incl}",
incl = txtInt(122),
.sep = "\n"))
grp_a <- boxGrob(glue("Treatment A",
"n = {recr}",
recr = txtInt(43),
.sep = "\n"))
grp_b <- boxGrob(glue("Treatment B",
"n = {recr}",
recr = txtInt(122 - 43 - 30),
.sep = "\n"))
excluded <- boxGrob(glue("Excluded (n = {tot}):",
" - not interested: {uninterested}",
" - contra-indicated: {contra}",
tot = 30,
uninterested = 12,
contra = 30 - 12,
.sep = "\n"),
just = "left")
grid.newpage()
vert <- spreadVertical(org_cohort,
eligible = eligible,
included = included,
grps = grp_a)
grps <- alignVertical(reference = vert$grps,
grp_a, grp_b) %>%
spreadHorizontal()
vert$grps <- NULL
excluded <- moveBox(excluded,
x = .8,
y = coords(vert$included)$top + distance(vert$eligible, vert$included, half = TRUE, center = FALSE))
for (i in 1:(length(vert) - 1)) {
connectGrob(vert[[i]], vert[[i + 1]], type = "vert") %>%
print
}
connectGrob(vert$included, grps[[1]], type = "N")
connectGrob(vert$included, grps[[2]], type = "N")
connectGrob(vert$eligible, excluded, type = "L")
# Print boxes
vert
grps
excluded
Based on r-bloggers
Documentation: https://www.r-bloggers.com/2018/05/flow-charts-in-r/
grid.newpage()
# set some parameters to use repeatedly
leftx <- .25
midx <- .5
rightx <- .75
width <- .4
gp <- gpar(fill = "lightgrey")
# create boxes
(total <- boxGrob("Total\n N = NNN",
x=midx, y=.9, box_gp = gp, width = width))
(rando <- boxGrob("Randomized\n N = NNN",
x=midx, y=.75, box_gp = gp, width = width))
# connect boxes like this
connectGrob(total, rando, "v")
(inel <- boxGrob("Ineligible\n N = NNN",
x=rightx, y=.825, box_gp = gp, width = .25, height = .05))
connectGrob(total, inel, "-")
(g1 <- boxGrob("Allocated to Group 1\n N = NNN",
x=leftx, y=.5, box_gp = gp, width = width))
(g2 <- boxGrob("Allocated to Group 2\n N = NNN",
x=rightx, y=.5, box_gp = gp, width = width))
connectGrob(rando, g1, "N")
connectGrob(rando, g2, "N")
(g11 <- boxGrob("Followed up\n N = NNN",
x=leftx, y=.3, box_gp = gp, width = width))
(g21 <- boxGrob("Followed up\n N = NNN",
x=rightx, y=.3, box_gp = gp, width = width))
connectGrob(g1, g11, "N")
connectGrob(g2, g21, "N")
(g12 <- boxGrob("Completed\n N = NNN",
x=leftx, y=.1, box_gp = gp, width = width))
(g22 <- boxGrob("Completed\n N = NNN",
x=rightx, y=.1, box_gp = gp, width = width))
connectGrob(g11, g12, "N")
connectGrob(g21, g22, "N")